Saturday, 12 September 2009

genetics - effect of background selection on promoter regions compared to distant enhancers?

Has anyone looked at the effect of background selection on the levels of conservation of promoter regions compared to distant enhancers? Do promoter regions have a higher conservation due to background selection from nearby genes compared to more distant enhancer regions?



My attempts to google for this only gave me a 2004 Drosophila paper on a few genes survey:



http://mbe.oxfordjournals.org/content/21/2/374.full



I am wondering if this has been looked at before or if there are any other relevant bits of genetics one should consider first.



EDIT: a bit more of explanation into the hypothesis below, and a reference that could be useful:



Let's start supposing a region near a coding gene that can gain regulatory potential via a new point mutation or small translocation. This new regulatory potential needs to be positively selected after it appears, or it will gradually accumulate more mutations and disappear. But if the region is close enough to the coding gene, recombination rate between the region and the nearby gene body will be low, proportional to their distance. If the gene body is assumed under selective constraint, there will be a hitchhiking effect of the nearby regulatory region by the gene nearby. The background levels of mutation on the regulatory region are then going to be lower (lower background mutation) than in a region that is not near a gene under strong selective constraint. So one way of explaining why close promoter/enhancer regions are more conserved than distant enhancer regions would simply be due to linkage.



A second part of the hypothesis would be about the presence or absence of recombination hotspots in upstream regions of a coding region: if nearby promoter/enhancers are kept via linkage to the closest gene, unbiased measures of cross-over (e.g. PRDM9 experiments in mouse testis) should indicate if there is an increased linkage of functional genomic blocks, like enhancer/promoter/gene blocks (Hi-C, 4C, 3C data), whereas if recombination doesn't play a role, regulatory blocks wouldn't necessarily be kept in the same haplotype block.

Friday, 11 September 2009

ecology - When are population dynamics models useful?

I'll throw one more application into the pot. Population dynamics also forms the foundations of population genetics, population ecology, and more recently plays an important role in frameworks such as evolutionary game theory and eco-evolutionary dynamics.



Here the models are also used as a type of theoretical exercise or thought experiment (as a previous answer suggests). In the development of evolutionary theory we simply cannot observe the process over the timescales we require to test the hypotheses we make. Thus, the development of population models allows us to explore 'possible worlds', as Robert May once put it, to see what kinds of adaptations or population structures we would expect to see, given the assumptions we put in.



We are also seeing an increasing number of population models and dynamical models used in conjunction with experiments on microbes in the field of experimental evolution. Here we can observe evolution in real time, and many of the assumptions about well-mixedness and large population sizes that are often made in modelling populations are actually fairly accurate.

Thursday, 10 September 2009

observation - Could science be lost if a phenomena is observed before predicted?

An observation could validate the predictions made by a previous theory. If something unpredicted is observed, then a new theory which is compatible with the observation should make predictions which later are confirmed by new observations.



But what if no such new predictions are possible to make? What is the scientific status of a theory which after the fact is only compatible with all data, but which cannot make any new predictions? If it would be considered weak, does this mean that discoveries through observation can actually destroy science?



Is this a valid argument for delaying the construction of better observatories until theories have matured given all existing data? Kind of comparable with the forward planetary protection argument which says that human spaceflight to Mars should wait until it is certain that there's no life there which could go extinct when it meets Earthly life.

geocentrism - How would the solar system look in a Geocentric model?

Only for Sun, Earth and Mars, but here's an interactive Flash that illustrates it graphically. Third link from the top "Part I, Equivalence of Hypotheses (Flash)" Note that the planets don't move as you move the mouse over the image, only the circles (the theory) change.
http://science.larouchepac.com/kepler/newastronomy/part1/MegaEquivalence.swf for the animation. More generally: http://science.larouchepac.com/kepler/newastronomy/
(And I don't know or care who that LaRouge Pacman is, some rich guy for some reason financed good explanations of what Kepler did, that's what I know about it and that's all very good)



If you move the mouse pointer to the upper left you get the heliocentric system. To the upper right you get the geocentric system. The point is to illustrate how Kepler proved that Ptolemy, Copernicus and Tycho all had the same mathematical model for the solar system. They just used different frames of reference to it, just choosing different fixpoints from where to view it.



Some dots in the illustration represent important points in that ancient model. Some of them are stand-ins for the foci of an ellipse in a model made out of perfect circles. And the Sun was actually not the center of the Copernican model, a point near the Sun was. According to Copernicus the Sun was just a decoration which randomly happened to hang around near the center. Kepler was the first to come up with the thought that maybe there is a relationship between the geometry and the physical existence of stuff. An idea later developed to the theory of gravity by Newton and Einstein, who just added to Kepler's initial formula for describing the movements of the planets.

Wednesday, 9 September 2009

Cluster of fast moving stars

It is highly likely that you might have observed an artificial satellite, most commonly of Iridium series which can flare as bright as -6 magnitude. You can have a check on it anytime. Heavens Above is one of the most trusted sources that can notify you depending on your location. Even NASA is having such service that can notify you about ISS passes. A dozen of mobile apps are there for assistance too.



If you think it was visible for a short time like meteors are, then you are free to report it here : AMS Fireball Report or here : IMO Fireball Report



Don't feel embarrassed if you might have mistaken a jet to that of a moving star. We all have faced that in our initial days of sky observation. Hope this helps

Tuesday, 8 September 2009

Approximate distance from Earth to Mars at a given moment with reasonable (+/-100km) accuracy?

Do not underestimate the astronomers! 100 km? That's absurd. Saturn('s center of mass) is located to within one mile's distance from the Sun. Mars is of course even much better located.



Here's a site I googled that seems to give current distance to Mars to within single kilometers. I don't know how that site makes up its numbers, but it is certainly possible to measure it like that. With mutual radio communication, there are really good opportunities for precis distance measuring. 135,834,832 km just now! Pretty close and that's why the ExoMars space probe was launched towards Mars a few days ago. And here is a table with the conunction distances just past and soon coming up.

Monday, 7 September 2009

solar system - Is there a photo that shows a iron meteor or asteroid in space in raw form having no layers of fusion crust?

In short, no.



The reason is that while finding meteorites on Earth is hard, finding them in space is a lot harder. A small asteroid, weighing only a few kg can't be spotted while it is still in space. The first we know of them is when they make their fiery descent.



On the other hand, there are some large asteroids that are metallic, such as 16 Psyche, and we have direct images of other large asteroids. Metallic asteroids are relatively rare, and have a higher albedo than stony asteroids, and much more than comets. However they are not shiny balls of metal. After a few billion years in space they absorb 80% of the light that falls on them.